Chromosome-based genome assembly for Culex quinquefasciatus

描述（由申请人提供）：蚊子是许多传染病的媒介。为了促进先进的基于基因组的病媒控制策略的发展，在过去的十年中，对三种主要蚊子属--按蚊、伊蚊和库蚊的基因组进行了测序。Cx的基因组组装。致倦丝虫是淋巴丝虫和脑炎病毒的主要载体，是最碎片化的，只有9%的基因组位于染色体上。缺乏一个高质量的，基于染色体的基因组组装的Cx。致倦库蚊是库蚊生物学和蚊子比较基因组学研究的一个障碍。使用Amplicon Express最近开发的下一代焦点基因组测序（FGS）方法，我们将获得2304个BAC克隆的~250 Mb高质量序列组装。序列与现有基因组的比对将大大提高基因组组装的质量。超重叠群的总数将从3171减少到约600。此外，我们的项目将开发一个新的Cx的细胞遗传学图谱。quinquefasciatus基于来自4龄幼虫的成虫盘的有丝分裂染色体，并将大多数基因组超重叠群锚到该图。这个R21提案的主要目标是显著改善Cx的基因组组装。致倦肌该项目的具体目标是：1）通过使用Focus Genome Sequencing（FGS）对2304个BAC克隆进行测序，提高基因组组装的质量; 2）通过将约1000个BAC克隆与Cx进行荧光原位杂交（FISH），创建基于染色体的基因组组装。致倦犬染色体Cx高质量基因组组装的可用性。quinquefasciatus将加强病媒生物学的研究。该项目的成果将通过矢量数据库传播。

DESCRIPTION (provided by applicant): Mosquitoes are vectors of numerous infectious diseases. To facilitate the development of advanced genome-based strategies for vector control, the genomes of the three major mosquito genera-Anopheles, Aedes, and Culex-were sequenced over the last decade. The genome assembly of Cx. quinquefasciatus, the major vector of the lymphatic filariasis worm and encephalitis viruses, is the most fragmented, with only 9% of the genome placed to the chromosomes. The lack of a high-quality, chromosome-based genome assembly for Cx. quinquefasciatus remains an impediment to further progress in Culex biology and comparative genomics of mosquitoes. Using the Next-Generation Focus Genome Sequencing (FGS) approach, recently developed by Amplicon Express, we will obtain ~250 Mb of high-quality sequence assemblies for 2304 BAC clones. Alignment of the sequences to the existing genome will greatly enhance the quality of the genome assembly. The total number of supercontigs will be reduced from 3171 to ~600. In addition, our project will develop a new cytogenetic map for Cx. quinquefasciatus based on mitotic chromosomes from imaginal discs of 4th instar larvae and anchor the majority of the genomic supercontigs to this map. The primary goal of this R21 proposal is to significantly improve the genome assembly for Cx. quinquefasciatus. The specific aims for this project are to: 1) improve the quality of the genome assembly by sequencing 2304 BAC clones using Focus Genome Sequencing (FGS) and 2) create a chromosome-based genome assembly by multicolor fluorescent in situ hybridization (FISH) of ~1000 BAC clones to Cx. quinquefasciatus chromosomes. The availability of a high-quality genome assembly for Cx. quinquefasciatus will enhance research in vector biology. Results of this project will be disseminated through VectorBase.